EFNA3

ephrin A3 | Ehk1-L, LERK3, EPLG3

This gene encodes a member of the ephrin (EPH) family. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, especially in the nervous system and in erythropoiesis. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. This gene encodes an EFNA class ephrin. [provided by RefSeq, Jul 2008]

Biological processes 18 terms

axon guidance (GO:0007411)cell-cell signaling (GO:0007267)ephrin receptor binding (GO:0046875)ephrin receptor binding (GO:0046875)ephrin receptor binding (GO:0046875)ephrin receptor signaling pathway (GO:0048013)ephrin receptor signaling pathway (GO:0048013)ephrin receptor signaling pathway (GO:0048013)ephrin receptor signaling pathway (GO:0048013)membrane (GO:0016020)negative regulation of angiogenesis (GO:0016525)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of amyloid precursor protein catabolic process (GO:1902993)protein binding (GO:0005515)transmembrane-ephrin receptor activity (GO:0005005)

Expression (TPM)

TFs regulating EFNA3 0 TFs

Transcription factors with Perturb-seq knockdown data for EFNA3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = EFNA3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to EFNA3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of EFNA3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr1:154,813,354–154,814,052	265.2 kb	Distal (>10kb) Multiome	189
chr1:154,870,031–154,870,680	208.5 kb	Distal (>10kb) Multiome	300
chr1:154,936,148–154,937,752	141.9 kb	Distal (>10kb) Multiome	1149
chr1:154,955,571–154,956,925	122.6 kb	Distal (>10kb) Multiome	504
chr1:154,961,269–154,962,529	117.1 kb	Distal (>10kb) Multiome	985
chr1:154,970,161–154,971,641	107.9 kb	Distal (>10kb) Multiome	535
chr1:154,972,362–154,975,914	104.2 kb	Distal (>10kb) Multiome	1085
chr1:154,982,968–154,983,632	95.6 kb	Distal (>10kb) Multiome	693
chr1:154,998,961–155,004,423	79.5 kb	Distal (>10kb) Multiome	1210
chr1:155,017,084–155,017,941	61.3 kb	Distal (>10kb) Multiome	1003
chr1:155,050,292–155,052,078	27.6 kb	Distal (>10kb) Multiome	948
chr1:155,061,415–155,064,552	14.9 kb	Distal (>10kb) Multiome	860
chr1:155,069,748–155,070,373	8.5 kb	Proximal (<10kb)	147
chr1:155,070,748–155,071,423	7.7 kb	Proximal (<10kb) Multiome	542
chr1:155,071,790–155,072,067	6.8 kb	Proximal (<10kb)	109
chr1:155,078,524–155,079,535	18 bp	At TSS Multiome	397
chr1:155,079,852–155,081,529	2.1 kb	Proximal (<10kb) Multiome	539
chr1:155,081,810–155,082,570	3.0 kb	Proximal (<10kb)	256
chr1:155,084,373–155,086,501	6.2 kb	Proximal (<10kb) Multiome	865
chr1:155,091,315–155,091,900	12.7 kb	Distal (>10kb) Multiome	594
chr1:155,126,247–155,126,903	47.6 kb	Distal (>10kb) Multiome	776
chr1:155,127,607–155,128,120	49.0 kb	Distal (>10kb) Multiome	578
chr1:155,135,100–155,136,750	57.0 kb	Distal (>10kb) Multiome	938
chr1:155,166,847–155,168,170	89.0 kb	Distal (>10kb) Multiome HiCAR	622
chr1:155,172,629–155,174,979	94.5 kb	Distal (>10kb) Multiome HiCAR	903
chr1:155,192,921–155,194,099	114.8 kb	Distal (>10kb) Multiome	755
chr1:155,194,230–155,195,403	116.1 kb	Distal (>10kb) Multiome	753
chr1:155,207,822–155,209,789	130.1 kb	Distal (>10kb) Multiome	826
chr1:155,226,522–155,227,197	147.7 kb	Distal (>10kb) Multiome	600
chr1:155,227,312–155,228,116	148.8 kb	Distal (>10kb) Multiome	688
chr1:155,244,103–155,245,349	165.9 kb	Distal (>10kb) Multiome	900
chr1:155,250,356–155,251,199	172.0 kb	Distal (>10kb) Multiome	605
chr1:155,255,032–155,255,921	176.7 kb	Distal (>10kb) Multiome	661
chr1:155,261,679–155,262,788	183.5 kb	Distal (>10kb) Multiome	921
chr1:155,272,928–155,274,098	194.7 kb	Distal (>10kb) Multiome	768
chr1:155,276,933–155,278,884	199.7 kb	Distal (>10kb) Multiome	749
chr1:155,308,291–155,309,348	229.9 kb	Distal (>10kb) Multiome	934
chr1:155,320,564–155,321,470	242.1 kb	Distal (>10kb) Multiome	341
chr1:155,322,680–155,325,643	245.5 kb	Distal (>10kb) Multiome	979

Genome Browser

Genomic view of the EFNA3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.